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If you own an XR250, many of these tips will apply, however, the carburator jet sizes will be different.
PLEASE ADD YOUR BIKE (eg. XR400) and LOCATION TO YOUR PROFILE.
It really helps others answer your questions.
ALL OF THE LINKS ARE BROKEN!!!
I will fix them as time allows.
Until then the Search Feature and enter "kevin's xr400 mods".
The results will bring up most of the links.
Here are some frequently asked questions I have answered before.
Which XR should I buy?
The longer the straights, the taller the hills, the deeper the sand; the bigger XR you want. The tighter the trail, the smaller hills, firmer terrain; the smaller XR you want.
The XR400 has a great motor that will pull you almost anywhere. You can be sloppy on a hill climb on an XR400, where you have to keep the 250 singing. The XR400 weight is most noticable when you drop it or try to stop it going down a long downhill. (Moooomentum!)
The XR250 feels like a mtn bike compared to the XR400. My friend rode his XR250 for years before decided he needed more power. Even then you can add a 300 kit and get good power.
If you were heading to ride fireroads in Baja, I'd tell you to get the 600/650.
To the tight woods, get the 250.
A lot of both, the 400.
Dual-sporting? Go bigger for more freeway, but don't show up at the trailhead with too big of a bike.
All of the XR's are great. Pick the one that fits your needs.
Gordon's Mods for XR400 (Uncorking the bottle up performance)
Gordon's Mods for XR400
XR400 History
The changes to the XR400 have been listed here several times. This list appears to be complete.
In addition, HairyScary discusses how to tell if a part has been updated by the part number. Good tip!
XR400 history
Getting the Spark plug out
It seems the MotionPro spark plug socket does not work on the XR400R, but works on the XR250R.
There is an OEM tool kit being sold on eBay that seems to work.
http://www.thumpertalk.com/forum/showthread.php?t=475545
717448 XR400 oil change
Here is a way to make changing the oil much cleaner.
This tips is really handy if you have a skid plate.
XR400 oil change
XR400 FAQ by Paul Gortmaker
Paul usually has very good info.
http://www.freewebs.com/hairyscary/XR400_FAQ.txt
Small bolts
BE CAREFULL with the bolts on the oil filter cover!
An oil covered bolt will not torque at the same rate as a dry bolt.
The friction doesn't build up, the force simply builds until the threads strip.
This is the reason many people strip out these bolts.
Here is an execllent website on bolts, oil, and misc values.
http://raskcycle.com/techtip/webdoc14.html
Did you ever wonder why a 8mm box wrench is half as long as a 18mm box wrench?
It is shorter as most 8mm bolts cannot take very much torque.
I highly recommend getting getting an 1/4" socket set.
I bought the Craftsman set at Orchard (owned by Sears), which tends to sell them for less.
What is the Snorkle?
http://www.4strokes.com/tech/honda/snorkel.asp
This place has a description and pic, it's easy after you pull the seat. I siliconed a piece of coarse screen (fiberglass) over mine to keep bugs and stuff out. - NORTEXT
717439 XR400/250 Pre-Filter
After pulling the snorkle, there is a big hole on the top of your XR400. My friend showed me this prefilter trick.
Pre-Filter
767409 XR400 Engine Bog, Pilot jet, and the Fuel Screw
On XR400's twisting the throttle from fully closed to wide open will cause the engine to "bog" or in some cases die.
Engine Bog, Pilot jet, and the Fuel Screw
831305 Valve adjustment (Am I retarded...)
Inspect and adjust valve clearance while the engine is cold (35C, 95F).
Valve adjustment
389095 bigger jets (Lists stock jet sizes.)
96-97 XR400's were jetted assuming you would remove the intake and exhaust snorkel.
98 and later XR's were jetted assuming you would leave them in.
bigger jets
739907 Cheap Tool for Setting the Fork Oil Height
There are some really nice tools out there for doing this job.
This tool costs $4.49 at Kragen.
Cheap Tool
392932 high altitude jetting
There are two big factors for jetting, elevation and temperature.
high altitude jetting
Allen screws for the XR400 carb
This lists the screws you need to convert the XR400 carb to use allen screws.
Allen screws
Screws for the brake and clutch after removing the stock handguards
TBD - There is a post with the shorter screw part numbers for after the stock handguards are removed. Use search.
Very quick engine hop up
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This is a very minimal change that should take less than an hour.
Most of that time is removing the float bowl (3 screws).
If you decide to do the full "Gordon's Mods" later, you will need to replace the jets again.
o Pull the intake snorkle.
o Add a UniFilter.
o Pilot jet to 55, main jet to 155. (Assuming sea level and moderate air temps.)
Source: Motocross Action magazine.
Quick engine hop up
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Gordon's mods
Baja Designs Baja Baffle with 96' spark arrestor.
Pull the intake snorkle, UniFilter, 60 pilot jet, 162 main jet.
(Depending on altitude and temp.)
What to add to a new XR400 or XR250?
------------------------------------
Acerbis wrap around style handguards (saves levers and bars as they don't dig in)
Baja Designs skid plate (Made by Utah Sports Cycle)
Acerbis fork/disc protector
Suspension
---------------
Grease headset and rear linkage
Spend you money on the suspension, not a pipe!
First get some stiffer fork springs (96-97, 98-99 years)
Fork revalve (cost: 2 qts of oil & time)
Shock revalve (cost: oil, nitrogen, shim stack, friend who knows shocks)
Jetting for Altitude (XR400)
----------------------------
Assuming at sea level and 68 degrees, you would use a 60 pilot and 162 main.
At 5000 feet and 68 degrees.
http://www.4strokes.com/tech/honda/carbadj.asp
Jettting correction:
5000 feet and 68 degrees.
Main 0.96 * 162 = 155 -> 155 main
Pilot 0.92 * 60 = 50.6 -> 55 pilot
Due to your elevation, you have less air and less fuel.
Your bike will not behave the same as a bike at sealevel.
First, check the fuel screw. If it does not affect the idle speed, you have the wrong one.
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kevin's xr400 mods

Can we make a sticky thread of pictures? I've done search for pics but I want to see all sorts of bikes just for ideas on stuff without having to go through tons of threads. Not trying to sound whiny or anything, but I think it would be nice to do what they do in the CRF250X forums with a sticky thread of just pics, no comments or anything. Think we can get one of those rolling here?

Ok guys, add one more to the list of riders attempting the USD fork swap to an XR frame. Quite a bit of research here on TT and ebay hunting brought me a pretty good deal on a set of forks, triples, and stem from a 00' CR 250.
There are a few different options for adapting CR style forks to an XR. Bushings for upper and lower CR triples can be made to allow use of the stock XR stem. Specialty bearings can also be purchased to allow use of the stock CR stem in the XR neck. And finally what seems to be the most common; modification of the stock CR stem to allow use of XR sized bearings.
I obviously chose to pursue the third option for a few reasons, the most prominent of which is serviceability. I wanted to keep as many wear items at possible as stock parts. This has two advantages; availability and price of replacement parts. $45 dollar a pop "specialty" thin section tapered bearings don't sound too appealing especially when being used on a 12 year old dirtbike.
So now we can get to the meat of the issue; modification of the CR stem. I should begin by saying that i am NOT a draftsman. I've taken a few classes on engineering measurements but am far from an expert and probably only mildly proficient reverse modeling components. With that said, the first order of business was comparing an XR stem and bearings to a CR stem and bearings. Shown below.

A little closer look at the XR setup.

And the CR setup.

Now to get out the calipers and model up the stock CR piece. I used a cheaper set of calipers and suspect their tolerance is +/- .01mm. Good enough for gov'ment work though! All dimensions in millimeters.

Now to modify the CR stem to work with the XR bearings while remaining compatible with CR triple trees. There are a few things to say about why i did some things the way i did but most of the thoughts are included in the notes section of the drawing.

With a resized stem we run into the problem of mounting the top triple clamp. The hole is too large for the stem. An insert bushing must be made to resize the hole in the clamp.

Finally what the stem and bushing look like together.

Last one. The difference in how the top triple clamp is located on the stem. The CR is equipped with a chamfer that provides a stop for the tree while the XR's triple appears to be limited only by the threads for the castle nut.

So... would like to hear your opinions on the execution of the stem modification and bushing. I think having these drawings will make it simpler to have the modifications performed as opposed to asking the machinist to completely reverse engineer the part him/herself.
And a final query: Anyone know the thread callout for the two threaded portion of a stock XR steering stem? My drawings show the outside diameter of the threaded portions and i have a cheap plastic pitch gauge that tells me a pitch of 1.0 but i am looking for something more concrete than what i have.
Thanks for your thoughts and opinions.

I'm on strike 2 here but thankfully this isn't baseball.
The reasoning and my history. If you haven't figured it out yet I've done a crap load of work on these motors over the last 7 years but they have had 4 wheels around them. In the EX world there are a lot of carburetor options and although many are great there's a cheap alternative that runs 95% as hard as the high dollar options, some even liking it better then aftermarket. When I joined up here in the 2 wheel club I was shocked that the only accepted option was $400 for a 36mm Mikuni Pumper that isn't any bigger then stock! That cheap alternative for the EX is an 04-05 trx450r carb. It's 42mm round slide Kiehin piston-valve with accelerator pump and a mildly modded 400 loves it with a surprisingly strong bottom end yet. Yes I said 42mm!
So as I build my XR4 I already know that I'd be shooting myself in the foot if I settled on a 36mm carb because I like bigger bores and cams and this motor likes bigger carbs. Makes sense, it is 400cc. Don't get me wrong though, the Mikuni is a real nice pumper for a stock bike and would seem fine on a well modded machine too but this 4 stroke is like every other one in the world in regards to when you go big inside, you want to go bigger outside or you're missing out.
Whether the info is appreciated or scoffed at I'll post up my findings one by one as I try to find viable alternatives. When I say viable I mean still being able to use the stock environment and not needing a ton of work. I'm sure collectively this is not a new idea to search for such a beast but I enjoy a good project and I like cheap alternatives when they produce results.
Currently the "test bike" is a 2000 Xr400r, snorkel removed, Uni filter, stock engine, stock headpipe and a 4" supertrapp slip-on with 11 discs.